org.biojava.bio.seq.distributed

Interface DistDataSource

All Known Implementing Classes:

GFFDataSource, SequenceDBDataSource

public interface DistDataSource

Object which contributes data to a DistributedSequenceDB.

DistDataSource is responsible for providing some information about what sequences exist, what the SymbolList associated with it and what features are here. Typically, the objects returned from DistributedSequenceDB will be composed from information from multiple DistDataSource instances.

Since:

1.2 Take an instance of this interface and add it to a DistributedSequenceDB. Implement this if you have information about some seqeunces but do not wish to or can not integrate this with the main sequence at source. For example, if you have some locally annotated features for SwissProt entries, you could create a DistDataSource providing just your features and let the DistDataSource API integrate these in software with a SwissProt sequence db provider. DistDataSource instances can provided sequence information and feature information. These are integrated seperately. To provide sequences, implement hasSequence(), getSequence() and ids(). ids(false).contains(id) should equal hasSequence(id). Features are provided by implementing hasFeatures(), and the two getFeatures() methods. In the case where hasFeatures() returns true, getFeatures() should return a FeatureHolder. If it is false, getFeatures() may raise a BioException. If these rules are not followed, the results are undefined and may not be consistent.

Author:

Thomas Down

Method Summary

Methods

Modifier and Type	Method and Description
FeatureHolder	getFeatures(FeatureFilter ff) Get all features matching a FeatureFilter provided by this DistDataSource.
FeatureHolder	getFeatures(String id, FeatureFilter ff, boolean recurse) Get all features matching a FeatureFilter on a Sequence with an ID and recurse flats.
Sequence	getSequence(String id) Get a Sequence object for an ID.
boolean	hasFeatures(String id) Find out if this DistDataSource can provide features on a sequence with a particular ID.
boolean	hasSequence(String id) Find out if this DistDataSource provides the sequence information for a sequence ID.
Set	ids(boolean topLevel) Get the complete set of sequence IDs provided by this DistDataSource.

Method Detail

hasSequence

boolean hasSequence(String id)
                    throws BioException

Find out if this DistDataSource provides the sequence information for a sequence ID.

Parameters:

id - the String id of a sequence

Returns:

true if this DistDataSource provides the primary sequence, false otherwise

Throws:

BioException

hasFeatures

boolean hasFeatures(String id)
                    throws BioException

Find out if this DistDataSource can provide features on a sequence with a particular ID.

Parameters:

id - the String id of a sequence

Returns:

true if this DistDataSource provides features for the sequence, false otherwise

Throws:

BioException

getFeatures

FeatureHolder getFeatures(FeatureFilter ff)
                          throws BioException

Get all features matching a FeatureFilter provided by this DistDataSource. You can simulate getFeatures(id, ff, recurse) by using the advanced FeatureFilter implementations.

Parameters:

ff - the FeatureFilter to search with

Returns:

a FeatureHolder with all matching filters

Throws:

BioException

getFeatures

FeatureHolder getFeatures(String id,
                        FeatureFilter ff,
                        boolean recurse)
                          throws BioException

Get all features matching a FeatureFilter on a Sequence with an ID and recurse flats. You can simulate getFeatures(ff) by adding the apropreate FeatureFilter implementations.

Parameters:

id - the ID of the Sequence

ff - the FeatureFilter to search with

recurse - true if we are to recurse the feature hierachy, false otherwise

Returns:

a FeatureHolder containing all feature matching

Throws:

BioException - if the features could not be fetched

getSequence

Sequence getSequence(String id)
                     throws BioException

Get a Sequence object for an ID.

Parameters:

id - the ID of the Sequence to fetch

Returns:

a Seqeunce if hasSequence(id) would return true

Throws:

BioException - if either the ID could not be resolved or if the sequence could not be fetched

ids

Set ids(boolean topLevel)
        throws BioException

Get the complete set of sequence IDs provided by this DistDataSource.

If the recurse flat is true, the IDs associated with the top level will be returned. However, if it is false, then IDs should be returned for all levels of an assembly hierachy including the top level IDs.

Parameters:

topLevel - if true, return top level IDs, otherwise all IDs

Returns:

a Set of String IDs

Throws:

BioException - if the IDs could not be fetched